Abstract P1-07-05: Clinical utility of twenty-five gene-expression profiling using LAMP method in early stage breast cancer
Authors: Yasue Tsuchida, Takaaki Ueda, Yuka Nagatake, Satoru Michiyuki, Miku Hattori, Masaki Sato, Norihiro Tomita, Naoki Kanomata, Hideko Yamauchi
Journal: Cancer Research (2023)

Abstract Background The 21-gene Recurrence Score (RS) (Oncotype DX®) is one of the most frequently used multigene assays to predict prognosis and response to treatment for estrogen receptor-positive breast cancer. Although the result of two prospective randomized trials, TAILORx and RxPONDER trial have increasingly established the clinical utility of Oncotype DX®, the cost and testing period are disadvantages especially in Asian countries. To overcome these disadvantages, we developed a new multi-gene assay using Loop-Mediated Isothermal Amplification (LAMP). We have previously selected a twenty-five genes set through comprehensive gene expression analysis of breast cancer samples from more than 500 cases (patent pending). Although these twenty-five genes are different from those used in conventional assays, their physiological functions are similar to those of Oncotype DX®, and it is expected that the results will be equivalent to Oncotype DX® as a predictor of prognosis and chemotherapeutic efficacy. This new assay can be performed in own institution, and the result can be obtained less than one hour. It can lead to significantly reduce costs and testing time compared to conventional assays. Based on these backgrounds, we constructed the prediction algorithm based on the new gene expression profiles using LAMP and evaluated its performance in this study. Methods Total RNA was extracted using Maxwell® RSC RNA FFPE Kit (Promega) from FFPE tumor samples of postoperative breast cancer tissue which Oncotype DX® have already tested in our institution between January 2009 to January 2021and was quantified by Reverse-transcription LAMP enabling one-step reaction from reverse transcription to amplification under isothermal condition (63°C). Samples were divided into three groups, low-RS (RS 0-10), RS-intermediate (RS 11-25) and RS-high (RS ≥26) based on Oncotype DX®-RS. Using the obtained mRNA amplification detection time as an explanatory variable and Oncotype DX®-RS as an objective variable, a prediction algorithm based on expression profiles based on LAMP method was constructed and evaluated its performance with 4-fold cross-validation. The prediction algorithm was trained using extreme gradient boosting (XGBoost) algorithm that parameters used default of R package “xgboost”. We also performed the quality analysis of mRNA excluded from this analysis due to poor mRNA quality. The percentage of mRNA above 200nt (DV200) was calculated by electrophoresis, and the correlation between the degree of mRNA degradation and the number of years of storage was calculated. Results Of the 221 cases which have tested Oncotype DX® during the study period, 90 samples were used in the analysis, and the remaining samples were excluded from this study due to poor mRNA quality. Of the 90 samples, 19 cases were RS-low, 42 cases were RS-intermediate, and 30 cases were RS-high, respectively. The correlation coefficient between Oncotype DX®-RS and our LAMP method-based predicted RS was r=0.911 (95%CI 0.900−0.921, p-value &amp;lt; 0.001). The overall concordance rate with the predicted risk of recurrence (high/intermediated/low-RS) was 0.9343 (95%CI: 0.9174-0.9486, p-value &amp;lt; 0.001). Regarding the quality analysis of mRNA excluded from this analysis, we found the inverse correlation between the degree of mRNA degradation and the storage periods, namely higher DV200 with shorter periods. In particular, there was less mRNA degradation in specimens that had been stored for less than one year. Conclusion Our new gene expression profiling by the LAMP method suggested to have same discriminately ability with Oncotype DX® to predict the risk of recurrence in early breast cancer patients. The duration of mRNA storage and the fixation time in the FFPE preparation process are suggested to be important for maintaining the quality of mRNA. We are planning to further studies with increase sample size and analyze the correlation with prognosis. Citation Format: Yasue Tsuchida, Takaaki Ueda, Yuka Nagatake, Satoru Michiyuki, Miku Hattori, Masaki Sato, Norihiro Tomita, Naoki Kanomata, Hideko Yamauchi. Clinical utility of twenty-five gene-expression profiling using LAMP method in early stage breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P1-07-05.